Biology Reference
In-Depth Information
loci of monocot genomes, which were used in some members of the palm family. A
70 kb sequence was obtained for Arecaceae plants by this process, which is equivalent
to 44% of the known complete genome of the date palm plastid. In this sequence, 66
variable number of tandem repeats (VNTR) were found in palms, 77% of which were
in the intergenic region, and the remaining in intronic sequences. The 51 polymorphic
mononucleotide microsatellites encountered within palm genera and species can be
compared with the 342 homopolymers of 7 bp or longer found in the complete chloro-
plast genome of
Phoenix dactylifera
.
9.4 Slow Evolution in Palms
A major problem in molecular phylogeny analysis of palms is the slow rate of evo-
lution in commonly used DNA regions for plant phylogeny research. In comparing
the
Adh
(alcohol dehydrogenase) gene sequences of palms and grasses
[9]
, Morton
et al. suggested the use of low-copy nuclear genes for phylogenetic research.
Palm sequences
[10]
evolve at 2.61
10
9
substitutions per synonymous site per
year, which is slower than most plant taxa. According to Gaut et al.
[10]
, grass
Adh genes evolve 2.5 times faster than palms at synonymous sites. Wilson, Gaut,
and Clegg
[11]
analyzed the restriction variations of five enzymes (BamHI, ClaI,
EcoR, HindIII, and HpaI) of 22 species of plastid DNA from five subfamilies of
palms and found a 5- to 13-fold reduction in substitution rates within palm fam-
ilies relative to annual plant taxa. Further details of this topic are described by
authors of
[12]
.
9.5 Sequence Variations Used in Molecular Phylogeny of
Plants [13-17]
Despite these limitations, a lot of work has been carried out using many nuclear
and plastid DNA variations for phylogeny research in palms. DNA markers used in
phylogeny of plants in general are RPB2
[13]
, ITS
[14]
, and plastid regions trnT-F,
rbcL
[15]
, ndhF
[16]
, and matK
[15,17]
. The RPB2 (RNA polymerase II) gene cata-
lyzes the synthesis of mRNA in nuclei. It is a single-copy highly conserved gene
and consists of 3.5 kb with 24 introns
[13]
. The length of the intron sequences dis-
plays polymorphism among species
[13]
, making it the best candidate for phylog-
eny research.
Because of its rapid evolution, despite being a high copy number gene, the ITS
(internal transcribed spacer) region
[14]
holds potential for plant phylogeny studies.
Conserved regions of two spacer regions, ITS1 and ITS2, which have repeats, are
useful in obtaining high-level relationships
[14]
. Of the plastid regions, the rapidly
evolving matK (maturaseK) gene and the integeneric spacer region between the trnL
and trnF (trnL-F) regions provide well-resolved and highly supported trees for other
plants
[15]
.
